The long-term future for Johnson Controls (JCI) is in batteries for hybrid and electric cars, and systems for building-wide energy efficiency. Not that the near-term future is so bad. What with the recovery, slow though it might be, in the global auto industry. Johnson Controls knows how to make auto batteries. Lots and lots of them at once while keeping costs under control. The company has a 35% share of the global lead acid auto battery market after all. And that’s important, as important as technology, when it comes to grabbing a big share of the next generation lithium-ion batteries that will power the hybrid and electric cars of coming decades. Not that the company has ignored technology: it’s joint venture with the Saft Groupe adds key experience in lithium battery systems. Batteries currently make up about 15% of sales, while building efficiency systems account for another 37% of revenue. In the company’s fiscal third quarter, reported in July, Johnson Controls swung to a profit after two consecutive quarters of losses on the strength of cost cutting. Gross margin climbed to 14.9%. The company also told Wall Street to expect stronger profits sequentially in the fourth quarter in both the  battery and building segments. As of September 8 I’m adding shares of Johnson Controls to the Jubak’s Picks portfolio with a target price of $31 a share by July 2010. (Full disclosure: I own shares of Johnson Controls in my personal portfolio.)